The problem is that either they've been tracking the Moira and had little trouble finding it, or they've been following the ship this whole time. Running will only prolong the inevitable.

[ If there were a chance at real escape, Cortana would consider the idea of running far more seriously. They have a crew of varied abilities, a handful of children, and most of them had nothing to do with what happened to the planet... But the ships here don't seem to work the same as they do where she's from--they can't escape using random coordinates and disappearing into slipspace.

Even if they could, she doesn't know everything about the tracking technology that might be possible in this universe. They could still be found. It sounds like running really would only make this whole mess take longer. ]

We may as well deal with it now. Running may simply anger them and, when they catch up, we may not get the courtesy of a warning before they attack.